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Papers on SpliceMiner and EVDB have been submitted for publication. Please check back for citing specifics.
SpliceMiner: a high-throughput database implementation of the NCBI Evidence Viewer for microarray splice variant analysis. Ari B. Kahn, Michael C. Ryan, Hongfang Liu, Barry R. Zeeberg, D. Curtis Jamison, John N. Weinstein. BMC Bioinformatics , 2007 Mar 5;8(1):75).
Background
There are many fewer genes in the human genome than there are expressed
transcripts. Alternative splicing is the reason. Alternatively spliced
transcripts are often specific to tissue type, developmental stage,
environmental condition, or disease state. Accurate analysis of microarray
expression data and design of new arrays for alternative splicing require
assessment of probes at the sequence and exon levels.
Description
SpliceMiner is a web interface for querying Evidence Viewer Database (EVDB).
EVDB is a comprehensive, non-redundant compendium of splice variant data for
human genes. We constructed EVDB as a queryable implementation of the NCBI
Evidence Viewer (EV). EVDB is based on data obtained from NCBI Entrez Gene
and EV. The automated EVDB build process uses only complete coding
sequences, which may or may not include partial or complete 5¹ and 3¹ UTRs,
and filters redundant splice variants. Unlike EV, which supports only
one-at-a-time queries, SpliceMiner supports high-throughput batch queries
and provides results in an easily parsable format. SpliceMiner maps probes
to splice variants, effectively delineating the variants identified by a
probe.
Conclusions
EVDB can be queried by gene symbol, genomic coordinates, or probe sequence
via a user-friendly web-based tool we call SpliceMiner
(http://discover.nci.nih.gov/spliceminer). The EVDB/SpliceMiner combination
provides an interface with human splice variant information and, going
beyond the very valuable NCBI Evidence Viewer, supports fluent,
high-throughput analysis. Integration of EVDB information into microarray
analysis and design pipelines has the potential to improve the analysis and
bioinformatic interpretation of gene expression data, for both batch and
interactive processing. For example, whenever a gene expression value is
recognized as important or appears anomalous in a microarray experiment, the
interactive mode of SpliceMiner can be used quickly and easily to check for
possible splice variant issues.
We would like to hear from you. You can reach the team via email.
SpliceMiner and EVDB were originally developed jointly by the Genomics and Bioinformatics Group (GBG) of LMP, NCI, NIH and George Mason University, Department of Bioinformatics and Computational Biology. It is now maintained and under continuing development by GBG.